Publications by authors named "Nikolaos Tairis"

6 Publications

  • Page 1 of 1

Genomic characterization of MICA gene using multiple next generation sequencing platforms: A validation study.

HLA 2020 10 21;96(4):430-444. Epub 2020 Aug 21.

Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.

We have developed a protocol regarding the genomic characterization of the MICA gene by next generation sequencing (NGS). The amplicon includes the full length of the gene and is about 13 kb. A total of 156 samples were included in the study. Ninety-seven of these samples were previously characterized at MICA by legacy methods (Sanger or sequence specific oligonucleotide) and were used to evaluate the accuracy, precision, specificity, and sensitivity of the assay. An additional 59 DNA samples of unknown ethnicity volunteers from the United States were only genotyped by NGS. Samples were chosen to contain a diverse set of alleles. Our NGS approach included a first round of sequencing on the Illumina MiSeq platform and a second round of sequencing on the MinION platform by Oxford Nanopore Technology (ONT), on selected samples for the purpose of either characterizing new alleles or setting phase among multiple polymorphisms to resolve ambiguities or generate complete sequence for alleles that were only partially reported in the IMGT/HLA database. Complete consensus sequences were generated for every allele sequenced with ONT, extending from the 5' untranslated region (UTR) to the 3' UTR of the MICA gene. Thirty-two MICA sequences were submitted to the IMGT/HLA database including either new alleles or filling up the gaps (exonic, intronic and/or UTRs) of already reported alleles. Some of the challenges associated with the characterization of these samples are discussed.
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http://dx.doi.org/10.1111/tan.13998DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7589345PMC
October 2020

AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies.

Bioinformatics 2020 08;36(15):4353-4356

Department of Pathology and Laboratory Medicine.

Summary: A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction (RSE) is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most appropriate capture oligos for targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer-dimers in a pooled experiment, is therefore necessary. Manual design and selection of oligos becomes very challenging, complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences used to target and capture the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization array processes. AnthOligo was tested by capturing the Major Histocompatibility Complex (MHC) of a random sample.The application provides users with a simple interface to upload an input file in BED format and customize parameters for each task. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http://antholigo.chop.edu.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa552DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7520035PMC
August 2020

Resolving MiSeq-Generated Ambiguities in HLA-DPB1 Typing by Using the Oxford Nanopore Technology.

J Mol Diagn 2019 09 4;21(5):852-861. Epub 2019 Jun 4.

Immunogenetics Laboratory, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania. Electronic address:

The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, form the basis for the additional ambiguities encountered at an increasing rate in clinical practice. HLA-DPB1 characterization, particularly, generates a significant percentage of ambiguities (25.5%), posing a challenge for accurate and unambiguous HLA-DPB1 genotyping. Phasing of exonic heterozygous positions between exon 2 and all other downstream exons has been the major cause of ambiguities. In this study, the Oxford Nanopore MinION, a third-generation sequencing technology, was used to resolve the phasing. The accurate MiSeq sequencing data, combined with the long reads obtained from the MinION platform, allow for the resolution of the tested ambiguities.
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http://dx.doi.org/10.1016/j.jmoldx.2019.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6734860PMC
September 2019

Characterization of 108 Genomic DNA Reference Materials for 11 Human Leukocyte Antigen Loci: A GeT-RM Collaborative Project.

J Mol Diagn 2018 09 26;20(5):703-715. Epub 2018 Jun 26.

Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.

The highly polymorphic human leukocyte antigen (HLA) genes, located in the human major histocompatibility complex, encode the class I and II antigen-presenting molecules, which are centrally involved in the immune response. HLA typing is used for several clinical applications, such as transplantation, pharmacogenetics, and diagnosis of autoimmune disease. HLA typing is highly complex because of the homology of HLA genes and pseudogenes and the extensive polymorphism in the population. The Centers for Disease Control and Prevention established the Genetic Testing Reference Materials Coordination Program (GeT-RM) in partnership with the genetics community to improve the availability of genomic DNA reference materials necessary for quality assurance of genetic laboratory testing. The GeT-RM together with three clinical laboratories and the Coriell Cell Repositories have characterized genomic DNA obtained from a panel of 108 cell lines for all HLA classic polymorphic loci: HLA-A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1, and DPB1. The goal was to develop a publicly available and renewable source of well-characterized genomic DNA reference materials to support molecular HLA typing assay development, validation, and verification, quality control, and proficiency testing. These genomic DNA samples are publicly available from the National Institutes of General Medical Science Repository at the Coriell Cell Repositories.
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http://dx.doi.org/10.1016/j.jmoldx.2018.05.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939753PMC
September 2018

Launching the Greek forensic DNA database. The legal framework and arising ethical issues.

Forensic Sci Int Genet 2011 Nov 18;5(5):407-10. Epub 2010 Sep 18.

Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece.

Since the creation of the first national DNA database in Europe in 1995, many European countries have legislated laws for initiating and regulating their own databases. The Greek government legislated a law in 2008, by which the National DNA Database of Greece was founded and regulated. According to this law, only DNA profiles from convicted criminals were recorded. Nevertheless, a year later, in 2009, the law was amended to permit the creation of an expanded database including innocent people and children. Unfortunately, the new law is very vague in many aspects and does not respect the principle of proportionality. Therefore, according to our opinion, it will soon need to be re-amended. Furthermore, prior to legislating the new law, there was no debate with the community itself in order to clarify what system would best suit Greece and what the citizens would be willing to accept. We present the current legal framework in Greece, we highlight issues that need to be clarified and we discuss possible ethical issues that may arise.
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http://dx.doi.org/10.1016/j.fsigen.2010.08.013DOI Listing
November 2011

Beta-carotene production and sclerotial differentiation in Sclerotinia minor.

Mycol Res 2003 May;107(Pt 5):624-31

Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26100 Patra, Greece.

Sclerotinia minor accumulates beta-carotene at levels dependent upon oxidative growth conditions and differentiation. Beta-carotene accumulation is 2.5-fold higher in differentiated mycelia at high than at low oxidative stress, and approx. 3-fold higher in differentiated than in undifferentiated mycelia. It is proposed that beta-carotene may be produced by the fungus to counteract oxidative stress that develops during growth. This is shown by the finding that exogenous beta-carotene at growth non-inhibiting concentrations causes a concentration-dependent reduction of oxidative stress (lipid and protein peroxidation) and sclerotial differentiation in this fungus. The data of this study support our hypothesis that sclerotial differentiation in phytopathogenic fungi may be induced by oxidative stress.
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http://dx.doi.org/10.1017/s0953756203007822DOI Listing
May 2003
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